ArticleNature methods2016
Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.
Article in Nature methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
91 citing papers in PubMed.
- Artificial Intelligence and Machine Learning in Mass Spectrometry-Based Proteomics and Metabolomics.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Global Profiling of Post-Translationally Modified Crustacean Neuropeptidome Trends Affiliated with Feeding Activity.Journal of the American Society for Mass Spectrometry · 2026Article
- End-to-end deep attention-based multitask pipeline for predicting uncertainty-quantified peptide properties from mass spectrometry data.Scientific reports · 2026Article
- Review
- The State of Peptide Detectability in Computational Proteomics and Guidelines for AI Applications.Computational and structural biotechnology journal · 2026Article
- Genomic, Proteomic, and Biochemical Study ofJournal of agricultural and food chemistry · 2025Article
- Alternate RNA decoding results in stable and abundant proteins in mammals.bioRxiv : the preprint server for biology · 2025Article
- Glycerol mediates crosstalk between metabolism and trafficking through the golgin Imh1.Nature structural & molecular biology · 2025Article
- Supervised Contrastive Learning Leads to More Reasonable Spectral Embeddings.Analytical chemistry · 2025Article
- The Future of a Myriad of Accelerated Biodiscoveries Lies in AI-Powered Mass Spectrometry and Multiomics Integration.Journal of mass spectrometry : JMS · 2025Article
- A pan-cancer atlas of therapeutic T cell targets.bioRxiv : the preprint server for biology · 2025Article
- TopLib: Building and Searching Top-Down Mass Spectral Libraries for Proteoform Identification.Analytical chemistry · 2025Article
- The phosphorylation of Pak1 by Erk1/2 to drive cell migration requires Arl4D acting as a scaffolding protein.Journal of cell science · 2025Article
- Targeting the ERK1/2 and p38 MAPK pathways attenuates Golgi tethering factor golgin-97 depletion-induced cancer progression in breast cancer.Cell communication and signaling : CCS · 2025Article
- Perspectives in computational mass spectrometry: recent developments and key challenges.Bioinformatics advances · 2025Article
- Post-translational modifications of proteins in cardiovascular diseases examined by proteomic approaches.The FEBS journal · 2025Review
- The Hunt Lab Guide to De Novo Peptide Sequence Analysis by Tandem Mass Spectrometry.Molecular & cellular proteomics : MCP · 2024Article
- The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF.Analytical chemistry · 2024Article
- Dear-PSM: A deep learning-based peptide search engine enables full database search for proteomics.Smart medicine · 2024Article
- Oxidative stress mediates nucleocytoplasmic shuttling of KPNA2 via AKT1-CDK1 axis-regulated S62 phosphorylation.FASEB bioAdvances · 2024Article
31 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
Abstract
Mass spectrometry (MS) is the main technology used in proteomics approaches. However, on average 75% of spectra analysed in an MS experiment remain unidentified. We propose to use spectrum clustering at a large-scale to shed a light on these unidentified spectra. PRoteomics IDEntifications database (PRIDE) Archive is one of the largest MS proteomics public data repositories worldwide. By clustering all tandem MS spectra publicly available in PRIDE Archive, coming from hundreds of datasets, we were able to consistently characterize three distinct groups of spectra: 1) incorrectly identified spectra, 2) spectra correctly identified but below the set scoring threshold, and 3) truly unidentified spectra. Using a multitude of complementary analysis approaches, we were able to identify less than 20% of the consistently unidentified spectra. The complete spectrum clustering results are available through the new version of the PRIDE Cluster resource (http://www.ebi.ac.uk/pride/cluster). This resource is intended, among other aims, to encourage and simplify further investigation into these unidentified spectra.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.